Turbo Tax calculates it right. Even though the total shows up as regular income on lines 3b and 7, If you have capital gains or qualified dividends the tax is not taken from the tax table but is calculated separately from Schedule D. The tax will be calculated on the Qualified Dividends and Capital Gain Tax Worksheet. It does not get filed with your return. In the online version you need to save your return as a pdf file and include all the worksheets to see it.
You can probably tell because the tax on 1040 will be less than the Tax Table.
